Bacteria and Archaea have been placed separately because their cells have differential compositions. Bacteria and Archaea are prokaryotes.
Archaea and Bacteria domains are prokaryotes because their cells do not contain membrane-bound organelles or cell nuclei.
However, there are certain phenotypic, structural, and evolutionary features to distinguish Archaea and Bacteria domains.
For example, the Archaea cell membrane contains isoprene hydrophobic groups and phospholipid linkages (it is not found in bacteria).
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